The hottest Genomics Substack posts right now

And their main takeaways
Category
Top Science Topics

Saturday Commentary and Review #126

Fisted by Foucault • 223 implied HN points • 27 May 23
🌍 World Politics Genomics
  1. Soviet Union's collapse due to economic and political reforms by Gorbachev.
  2. Saudi Arabia's modernization efforts under MBS involve economic restructuring and social liberalization.
  3. US lagging behind China in 5G tech adoption due to regulatory obstacles and internal disagreements.

Stream Genomics - Cameras

ASeq Newsletter • 14 implied HN points • 28 Jul 25
🕹 Technology Genomics
  1. Stream Genomics uses special cameras that capture changes in pixels instead of taking regular still images. This helps in detecting fast events more effectively.
  2. These cameras have higher dynamic range, meaning they can handle bright lights without losing details. They also produce less noise compared to regular cameras, which makes imaging clearer.
  3. There's still some uncertainty about how much these cameras can help in reducing noise for tasks like single molecule sequencing, but they show promise for better signal detection.

Microarrays: What are they for?

ASeq Newsletter • 36 implied HN points • 11 Feb 25
🔬 Science Genomics
  1. Microarrays are often seen as an alternative to sequencing, but some argue sequencing is generally a better option for many applications. It's important to consider these viewpoints when discussing the technologies.
  2. The microarray market is stable, worth around $1 billion, with platforms like Illumina's Beadarray holding a significant share. This indicates that there is still a solid demand for microarray technology.
  3. Reassessing biases about technologies like microarrays can help us understand their current relevance and future potential. It’s always a good idea to keep an open mind when evaluating scientific tools.

Illumina@JPM - More Clinical!

ASeq Newsletter • 29 implied HN points • 15 Jan 25
🕹 Technology Genomics
  1. Illumina's revenue has been flat but they are focusing on clinical applications, now making up 56% of their market. This indicates a shift in strategy towards health-related services.
  2. The company continues to reduce its cost per gigabyte of sequencing, although it remains higher than some competitors. They're positioning themselves to provide more value and insights rather than just cheaper sequencing.
  3. Despite the competitive pressure on pricing, Illumina aims to deliver high-quality insights at a lower overall cost instead of racing to the bottom with pricing like some other vendors.

Oxford Nanopore

axialdaily • 19 implied HN points • 17 Mar 23
🕹 Technology Genomics
  1. Oxford Nanopore sequences DNA with a nanopore technology.
  2. ONT has made advancements in base-calling and chemistry for improved accuracy.
  3. The company has created a new genomics category and is exploring various applications beyond COVID surveillance.
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Roche: Where NGS Goes To Die...

ASeq Newsletter • 21 implied HN points • 03 Feb 25
🕹 Technology Genomics
  1. Roche has a history of acquiring new technologies, like the 454 sequencer, but often fails to support them properly, leading to their demise.
  2. Despite having potential with longer read capabilities, the 454 sequencer couldn't compete with faster competitors like Illumina, which changed market dynamics.
  3. Roche's failed attempts to acquire Illumina show their struggle to keep up in the competitive NGS market, further damaging their reputation.

A Little More Roche Information...

ASeq Newsletter • 21 implied HN points • 29 Jan 25
🔬 Science Genomics
  1. Roche is developing a new nanopore sequencer, which is creating some buzz in the scientific community. People are eager to hear more about its features and capabilities.
  2. Alex Dickinson shared his thoughts on Roche's new sequencer after a private briefing. His insights mostly echoed what is already known but added some new expectations for the upcoming announcement.
  3. A few individuals, including the author, have decided to skip NDA previews, allowing them to speculate freely about the product. This has led to informal discussions and excitement about what might be revealed soon.

Interview with Daniel MacArthur

The Good Science Project • 26 implied HN points • 02 Dec 24
🔬 Science Genomics
  1. Daniel MacArthur is working on making genomic medicine fairer for all communities. His research includes studying genetic differences in underrepresented groups to improve health outcomes.
  2. He believes that funding for science needs to be more flexible and stable. This would allow researchers to take risks and pursue long-term projects without the constant pressure of grant deadlines.
  3. MacArthur thinks research organizations should be built specifically to support scientific work. Many current institutions are not designed for research, making it harder for scientists to succeed.

Landscape of Sequencing-based Spatial RNA Technology

LatchBio • 15 implied HN points • 27 Feb 25
🕹 Technology Genomics
  1. Spatial RNA technology helps us see how cells interact in their natural environment. It gives a clearer picture than traditional methods that just show gene activity without their locations.
  2. There are many ways to capture and analyze spatial gene data, like using specially barcoded slides or microfluidic methods. Each approach has its pros and cons depending on what researchers want to study.
  3. Advancements in technology are making it possible to analyze tiny details, like individual cells or even parts of cells. This opens new doors for understanding biology and diseases.

All The DNA Sequencing Companies

ASeq Newsletter • 14 implied HN points • 17 Feb 25
🔬 Science Genomics
  1. There are many active DNA sequencing companies, and the list is always changing. Some companies that were once popular are now gone.
  2. Significantly, more DNA sequencing companies are now based in China than before. The landscape has shifted with around 15 out of 40 companies being Chinese.
  3. It's essential to stay updated about these companies as new ones emerge and old ones disappear. Sharing information can help keep track of these changes.

Another Nanopore: PolySeq

ASeq Newsletter • 14 implied HN points • 16 Feb 25
🔬 Science Genomics
  1. PolySeq is creating a new DNA/RNA sequencing tool similar to the Oxford Nanopore. It aims to improve how we sequence genetic materials.
  2. The device weighs 1.5 kilograms and can handle 2560 wells or pores. This design helps it generate a lot of data in a short time.
  3. PolySeq plans to produce 15 to 20 gigabytes of data in just 48 hours, making sequencing faster and more efficient.

An Ultima Genomics Sample Dataset

ASeq Newsletter • 51 implied HN points • 20 Nov 23
🔬 Science Genomics
  1. Ultima Genomics focuses on ultra-high throughput sequencing at a lower cost compared to Illumina.
  2. Data quality in Ultima's release is slightly worse than Illumina, but could still be sufficient for most applications.
  3. It will be interesting to see how Ultima performs in the market and how Illumina responds.

Year In Review - Everything Else!

ASeq Newsletter • 14 implied HN points • 20 Dec 24
🔬 Science Genomics
  1. Clinical sequencing is becoming a major part of the medical field, especially in areas like oncology and genetic disease testing. However, many clinicians still find it challenging to use these new testing methods.
  2. Protein sequencing is an emerging area with potential advancements on the horizon, particularly with new technologies like Nanopore. It's an exciting field that many are watching closely.
  3. Single cell analysis remains a hot topic, but companies like 10X Genomics are facing challenges with growth and patent issues. There are still many experiments and innovations happening in this space.

Some Thoughts On 10X Genomics

ASeq Newsletter • 36 implied HN points • 18 Jan 24
🔬 Science Genomics
  1. Spatial revenue for 10X Genomics is increasing, while single cell revenue growth is slowing down.
  2. There may not be much growth expected in single cell applications for 10X Genomics, but spatial sequencing shows potential for growth.
  3. 10X Genomics faces competition in the single cell market, but may retain a significant market share.

Functional protein mining with conformal guarantees

Axial • 14 implied HN points • 28 Nov 24
🔬 Science Genomics
  1. A new method is developed for predicting protein functions using something called conformal prediction. This makes the predictions more reliable and provides a clear way to understand risks when selecting proteins.
  2. The approach helps in annotating genes and predicting enzyme functions more accurately without needing new training models. This is great for speeding up research in life sciences.
  3. It also offers a smart way to reduce the number of proteins needing full analysis, making the process quicker and cheaper while still keeping good accuracy.

You can now run single-cell experiments in a tube with 4.5 hours of hands-on time

LatchBio • 12 implied HN points • 26 Dec 24
🕹 Technology Genomics
  1. A new single-cell sequencing technology makes experiments easier and faster, only needing about 4.5 hours of hands-on work. This means more scientists can do these experiments without needing a big budget or lots of extra equipment.
  2. The new method allows for better scalability, letting researchers run from 1 to 96 samples easily. This flexibility can lead to more data and insights in various experiments, such as drug development or studying disease.
  3. The SimpleCell technology also includes user-friendly analysis tools, making it easier for scientists to understand and visualize their results. This helps them feel more in control of their research and get valuable insights quickly.

I Don't Know How Long A Revio Run Takes...

ASeq Newsletter • 29 implied HN points • 06 Mar 24
🔬 Science Genomics
  1. The estimated time for a Revio run is around 35 hours.
  2. Pre-extension process is crucial as it helps prevent template breakage and increases overall yield of good polymerases/templates.
  3. The on instrument adaptive loading time in Revio can be set to a 2-hour limit.

The PacBio Benchtop - The Vega

ASeq Newsletter • 14 implied HN points • 07 Nov 24
🕹 Technology Genomics
  1. The new PacBio Vega is a benchtop DNA sequencer that provides 60Gb of data in just 24 hours and costs $169,000. There's also a lower cost option for labs that need less capacity.
  2. When compared to Oxford Nanopore's PromethION, the Vega appears to deliver better accuracy and more consistent results, making it a suitable choice for smaller labs needing reliable output.
  3. The launch of the Vega could help PacBio increase revenue and broaden its market presence, as it appeals to labs that want access to high-quality sequencing without breaking the bank.

Western Civilization And Genomics

ASeq Newsletter • 14 implied HN points • 06 Nov 24
🔬 Science Genomics
  1. Western civilization has thrived for about 2500 years, with many achievements in science and knowledge. This long history has shaped our understanding of complex topics like genomics.
  2. Key figures like Isaac Newton helped establish scientific methods, moving society away from superstition to rational thinking. This paved the way for discoveries in inheritance and DNA.
  3. Today, we can sequence human genomes more easily than ever before. This ability can change how we understand our biology and ourselves in profound ways.

Horrors Of The Theoretical Maximum

ASeq Newsletter • 14 implied HN points • 30 Oct 24
🕹 Technology Genomics
  1. Vendors sometimes quote theoretical maximums for data output, which can be misleading. It's important to understand that these numbers might not reflect actual performance.
  2. Comparing different technologies can be complicated because they have different specifications and capabilities. Each technology, like PacBio, Oxford Nanopore, and Illumina, has its unique strengths and limitations.
  3. In the real world, the difference between what is theoretically possible and what is actually achieved can be significant. This means we should be cautious and not rely solely on theoretical figures.

The Future of Sequencing

ASeq Newsletter • 29 implied HN points • 04 Jan 24
🔬 Science Genomics
  1. Sequencers should be as boring and simple as qPCR machines for easy use and accessibility.
  2. Automation in sequencing should focus on sample-to-answer approaches like the GeneXpert in diagnostics.
  3. Broader adoption of sequencing in clinical applications may require a cultural shift towards valuing diagnosis even without immediate treatment options.

All About The MiSeq

ASeq Newsletter • 36 implied HN points • 04 Sep 23
🔬 Science Genomics
  1. The MiSeq is one of Illumina's longest read sequencers.
  2. Illumina released the MiSeq to compete with Ion Torrent sales.
  3. The MiSeq is the oldest next-gen sequencer in the market, released in 2011.

DNA Tubes - The HiSeq X Fluidic System

ASeq Newsletter • 29 implied HN points • 13 Dec 23
🔬 Science Genomics
  1. The HiSeq X DNA sequencer contains about 100 meters of tubing inside for its fluidics system.
  2. The majority of the tubing in the HiSeq X appears to be around 1.5mm OD and 1mm ID, possibly made of PTFE.
  3. The fluidic path of the HiSeq X is structured similarly to the Solexa Genome Analyzer and uses components from the same vendors.

Roche Nanopore: Accuracy

ASeq Newsletter • 7 implied HN points • 28 Feb 25
🔬 Science Genomics
  1. Roche's Q39 accuracy system is different from other platforms like Illumina and Oxford Nanopore. It's important to compare them carefully as each has unique metrics.
  2. The average accuracy of different sequencing platforms varies, but Roche doesn't provide clear comparisons. They share limited data about their simplex accuracy.
  3. Understanding the differences in data quality and error rates across platforms is crucial. Factors like read length and error filtering play a significant role in the accuracy of sequencing results.

What The H*ll Is PPMSeq?

ASeq Newsletter • 21 implied HN points • 17 Feb 24
🔬 Science Genomics
  1. PPMSeq is a duplex sequencing technique that ensures high accuracy reads by reading both forward and reverse strands of a double-stranded sequence.
  2. Ultima's PPMSeq works by amplifying both strands on the same bead and utilizing a tag to identify their presence, with errors causing radical dephasing which is taken care of by downstream software.
  3. Approaches to implementing PPMSeq on Ultima's platform involve reading both strands in both directions simultaneously or keeping the product on beads in the same orientation, each with its own challenges and considerations.

Real-time Spatial Sequencing

ASeq Newsletter • 21 implied HN points • 25 Jan 24
🔬 Science Genomics
  1. Real-time spatial sequencing involves obtaining a full time course of RNA as it's transcribed and cleared from cells.
  2. Challenges include releasing RNA from cells without damaging them, determining porous array density, and developing a sequencing method.
  3. Potential solutions include using electroporation or biological nanopores, adjusting array density, and utilizing real-time sequencing approaches.

Ultima Genomics

ASeq Newsletter • 7 implied HN points • 17 Jan 25
🔬 Science Genomics
  1. Ultima Genomics is making progress, but there are doubts about their ability to meet demand.
  2. They have created a large dataset of 100 million cells with Vevo Therapeutics using new technology.
  3. The community is actively discussing their projects and updates to stay informed.

Rapid proteome-wide prediction of lipid-interacting proteins through ligand-guided structural genomics

Axial • 7 implied HN points • 05 Jan 25
🔬 Science Genomics
  1. Researchers developed a new tool called SLiPP that helps quickly find proteins that interact with lipids. This is important because lipids play key roles in cell functions and diseases.
  2. SLiPP uses machine learning to distinguish between protein pockets likely to bind lipids and those that won't. This makes it easier to identify potential targets for drug discovery.
  3. The tool has been successfully tested on different organisms, showing it can accurately predict lipid-binding proteins. This helps scientists explore new areas in lipid biology and disease research.

Even Enzymes Evolve

A Biologist's Guide to Life • 24 implied HN points • 30 Sep 23
🔬 Science Genomics
  1. Enzymes evolve through mutations in DNA that lead to changes in proteins.
  2. Proteins define traits, and understanding their evolution helps us comprehend life's diversity.
  3. Evolutionary biology provides a framework for understanding genetic changes in organisms, including the origin of antibiotic resistance.

Year In Review - Long Reads

ASeq Newsletter • 7 implied HN points • 18 Dec 24
🕹 Technology Genomics
  1. PacBio faced challenges in the stock market but still aims to provide high-quality clinical genomic sequencing. They are seen as a strong competitor in the long-read space despite financial struggles.
  2. Oxford Nanopore has been active in raising funds but has dealt with internal issues and departures of significant team members. Profitability remains an elusive goal for both them and PacBio.
  3. New competitors are emerging in the long-read sequencing market, including Roche and BGI, who are exploring nanopore sequencing technology. This could shake up the landscape for current players.

About v1

The Century of Biology • 27 implied HN points • 04 May 23
🔬 Science Genomics
  1. The rapid progress of biology is driven by advancements in DNA technology and communication.
  2. The newsletter aims to highlight exciting new research in genetics, genomics, and bioinformatics.
  3. The newsletter does not focus on peer review but instead aims to share exciting discoveries and findings.

Axial Discovery - Kidney disease

Axial • 29 implied HN points • 06 Mar 23
🏥 Health & Wellness Genomics
  1. Over 30 million people in the US are affected by kidney disease, leading to high healthcare costs and lowered quality of life.
  2. New tools like genomics, proteomics, and metabolomics are transforming drug development for kidney diseases.
  3. Companies like Goldfinch Bio and Chinook Therapeutics are developing medicines for rare kidney diseases with defined clinical milestones.

Let's Buy Singular Genomics!

ASeq Newsletter • 21 implied HN points • 13 Aug 23
🕹 Technology Genomics
  1. Singular Genomics is struggling with low share price and few instrument sales.
  2. Proposed solution is to develop a cheap MiSeq-class sequencer to target the lower end of the market.
  3. By focusing on cost-effective instrument with minimal field support, the company aims to attract small labs and researchers.

Ultima Unpatterned Flowcells

ASeq Newsletter • 14 implied HN points • 14 Feb 24
🔬 Science Genomics
  1. Ultima has transitioned to using unpatterned flowcells, which are cheaper and possibly work well with minor drawbacks.
  2. Ultima's manufacturing using unpatterned flowcells involves surface treatment and spin coating to attach and shrink beads for better identification and access.
  3. The occupancy and loading efficiency of Ultima's unpatterned flowcells suggest a potential capacity for 8 billion reads per run, showing advancements since their 2022 preprints.

An Illumina Sequencer In The Year 2000?

ASeq Newsletter • 14 implied HN points • 02 Feb 24
🔬 Science Genomics
  1. With proper investment, Illumina-style sequencing could have been developed 6 years earlier.
  2. Access to capital was crucial for the success of sequencing technologies.
  3. Investors prioritize attracting next round investments over the fundamental value of technology.

PacBio Market Cap <$1B

ASeq Newsletter • 7 implied HN points • 18 Mar 24
🕹 Technology Genomics
  1. PacBio's market cap drops below $1B, making it potentially attractive for acquisition.
  2. Despite some positives like new instruments and competitive specs, PacBio faces challenges in gaining traction for long-read sequencing in clinical settings.
  3. The majority of PacBio's IP expires in 2029, raising concerns that competitors could enter the market in the near future.